6H2J
Crystal structure of the HsdR subunit of the EcoR124I restriction enzyme with the C-terminal domain
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 1 UL OF PROTEIN IN 20 MM PHOSPHATE PH 7.5, 100 MM KCL, 5 MM ATP WAS MIXED WITH 2 UL OF RESERVOIR, CONTAINING 0.2 M LI2SO4, 8 % PEG 20K, 8 % PEG 550 MME, 1.5 MM DTT |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.68 | 54.09 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 123.91 | α = 90 |
b = 129.922 | β = 90 |
c = 161.01 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARRESEARCH | 2006-10-20 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X12 | 0.987 | EMBL/DESY, HAMBURG | X12 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||||||
1 | 2.6 | 20 | 100 | 18.2 | 9.4 | 80316 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.6 | 2.64 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2w00, 5j3n | 2.6 | 19.968 | 1.33 | 80202 | 977 | 99.93 | 0.2035 | 0.2027 | 0.2638 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 5.413 |
f_angle_d | 1.008 |
f_chiral_restr | 0.053 |
f_bond_d | 0.009 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14917 |
Nucleic Acid Atoms | |
Solvent Atoms | 383 |
Heterogen Atoms | 64 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
Auto-Rickshaw | phasing |